Have had that problem all the time, unplug it in the morning, and 30 minutes later, it's down to 95%. Turn it off and restart it, and it's back at 100%.
Maybe it's a bug in the calibration software/hardware? Who knows, but i've discharged it fully, charged it to 100% and it still does it. Just means every now and again i reboot it and it seems to work fine for a while, plus it only takes a minute or so to shutdown and reboot.
Every iPhone I have had has done that, even after calibrating the battery. Only fixed I have come across is to shutdown the phone and turn it back on, it's not hurting anything so it's never bothered me much but I wish apple would fix it.